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<a href="#pub-types">Public Types</a> &#124;
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<p><code>#include &lt;<a class="el" href="_sequence_file_reader_8hpp_source.html">SequenceFileReader.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a8cc42e15f26ed4a680ac4b968f0922a7"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> { <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1">dna</a>, 
<a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41">amino</a>, 
<a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7a9388aafb7eda9f884eed4c4dc315cc24">null</a>
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<tr class="memitem:a38d7a5bd2e01b009daa2fa7f0909ed57"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">fileType</a> { <a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2">fasta</a>, 
<a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c">stockholm</a>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:afefc977e0ab5e10c56afbf0f2fa2ada8"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#afefc977e0ab5e10c56afbf0f2fa2ada8">SequenceFileReader</a> (std::string *filename, <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> alphTypeIn)</td></tr>
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<tr class="memitem:a68f93cafb0fff8017a6ddfdac763b2ec"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a68f93cafb0fff8017a6ddfdac763b2ec">~SequenceFileReader</a> ()</td></tr>
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<tr class="memitem:ac6ddf2c86a6e8c25f21d9e1381cb08ce"><td class="memItemLeft" align="right" valign="top">std::string **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#ac6ddf2c86a6e8c25f21d9e1381cb08ce">getSeqs</a> () const</td></tr>
<tr class="separator:ac6ddf2c86a6e8c25f21d9e1381cb08ce"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a90a7fe721e3311573775ab8f7c946ec9"><td class="memItemLeft" align="right" valign="top">std::string **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a90a7fe721e3311573775ab8f7c946ec9">getNames</a> () const</td></tr>
<tr class="separator:a90a7fe721e3311573775ab8f7c946ec9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a19cd3893e28924779bfcb74a1cece03b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a19cd3893e28924779bfcb74a1cece03b">getAlphType</a> () const</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr class="memitem:a4ed189180afd320f49605425fad1a0d9"><td class="memItemLeft" align="right" valign="top">std::string **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a4ed189180afd320f49605425fad1a0d9">seqs</a></td></tr>
<tr class="separator:a4ed189180afd320f49605425fad1a0d9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ac5ad200019599845c0f1bc226ce0161b"><td class="memItemLeft" align="right" valign="top">std::string **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#ac5ad200019599845c0f1bc226ce0161b">names</a></td></tr>
<tr class="separator:ac5ad200019599845c0f1bc226ce0161b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a9318592fe459d2b67d3fb191b1f75057"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a9318592fe459d2b67d3fb191b1f75057">alphType</a></td></tr>
<tr class="separator:a9318592fe459d2b67d3fb191b1f75057"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aac56176cc7a6ed92728a106576ec3382"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#aac56176cc7a6ed92728a106576ec3382">numSeqs</a></td></tr>
<tr class="separator:aac56176cc7a6ed92728a106576ec3382"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5599fbffb34bd065bfb846947c6e9c41"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">fileType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_sequence_file_reader.html#a5599fbffb34bd065bfb846947c6e9c41">filetype</a></td></tr>
<tr class="separator:a5599fbffb34bd065bfb846947c6e9c41"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<h2 class="groupheader">Member Enumeration Documentation</h2>
<a id="a8cc42e15f26ed4a680ac4b968f0922a7"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8cc42e15f26ed4a680ac4b968f0922a7">&#9670;&nbsp;</a></span>AlphabetType</h2>

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          <td class="memname">enum <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">SequenceFileReader::AlphabetType</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a8cc42e15f26ed4a680ac4b968f0922a7aeafabf791da5b60629a8c2eea71c9ee1"></a>dna&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41"></a>amino&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a8cc42e15f26ed4a680ac4b968f0922a7a9388aafb7eda9f884eed4c4dc315cc24"></a>null&#160;</td><td class="fielddoc"></td></tr>
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<a id="a38d7a5bd2e01b009daa2fa7f0909ed57"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a38d7a5bd2e01b009daa2fa7f0909ed57">&#9670;&nbsp;</a></span>fileType</h2>

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          <td class="memname">enum <a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">SequenceFileReader::fileType</a></td>
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<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a38d7a5bd2e01b009daa2fa7f0909ed57a04f278c472cd9257e9f801c8094076a2"></a>fasta&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="a38d7a5bd2e01b009daa2fa7f0909ed57a71d055fafc2c7e7bda14e4aa68119a9c"></a>stockholm&#160;</td><td class="fielddoc"></td></tr>
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<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="afefc977e0ab5e10c56afbf0f2fa2ada8"></a>
<h2 class="memtitle"><span class="permalink"><a href="#afefc977e0ab5e10c56afbf0f2fa2ada8">&#9670;&nbsp;</a></span>SequenceFileReader()</h2>

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          <td class="memname">SequenceFileReader::SequenceFileReader </td>
          <td>(</td>
          <td class="paramtype">std::string *&#160;</td>
          <td class="paramname"><em>filename</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a>&#160;</td>
          <td class="paramname"><em>alphTypeIn</em>&#160;</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a68f93cafb0fff8017a6ddfdac763b2ec">&#9670;&nbsp;</a></span>~SequenceFileReader()</h2>

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<h2 class="groupheader">Member Function Documentation</h2>
<a id="a19cd3893e28924779bfcb74a1cece03b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a19cd3893e28924779bfcb74a1cece03b">&#9670;&nbsp;</a></span>getAlphType()</h2>

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          <td class="memname"><a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">SequenceFileReader::AlphabetType</a> SequenceFileReader::getAlphType </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a90a7fe721e3311573775ab8f7c946ec9">&#9670;&nbsp;</a></span>getNames()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ac6ddf2c86a6e8c25f21d9e1381cb08ce">&#9670;&nbsp;</a></span>getSeqs()</h2>

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<h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a9318592fe459d2b67d3fb191b1f75057">&#9670;&nbsp;</a></span>alphType</h2>

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          <td class="memname"><a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">AlphabetType</a> SequenceFileReader::alphType</td>
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          <td class="memname"><a class="el" href="class_sequence_file_reader.html#a38d7a5bd2e01b009daa2fa7f0909ed57">fileType</a> SequenceFileReader::filetype</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ac5ad200019599845c0f1bc226ce0161b">&#9670;&nbsp;</a></span>names</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#aac56176cc7a6ed92728a106576ec3382">&#9670;&nbsp;</a></span>numSeqs</h2>

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<hr/>The documentation for this class was generated from the following files:<ul>
<li>NINJA/<a class="el" href="_sequence_file_reader_8hpp_source.html">SequenceFileReader.hpp</a></li>
<li>NINJA/<a class="el" href="_sequence_file_reader_8cpp.html">SequenceFileReader.cpp</a></li>
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